I 100% agree with everything you're saying. Markdown is spectacular and the fragmentation out there is doing it an extreme disservice.
I've been using Markdown for notes, documentation and even for writing essays. If markdown could be adopted by Google for Sites and by Evernote, I think it would take over the world.
With that being said, a friend is writing a book and showed me AsciiDoc (http://www.methods.co.nz/asciidoc/) which is like a way-complicated markdown, but adds a lot of nice features for basic formatting that I think Markdown is missing for longer documents. If I were to write a book, I'd probably draft it in Markdown, but then spend a week wrangling it into some other format (asciidoc? TeX?) so that it pages and footnotes properly.
A quick search in the comments and someone else mentioned asciidoc, too. The beat me to it.

Markdown is a simple little humane markup language based on time-tested plain text conventions from the last 40 years of computing. Meaning, if you enter this… …you get this! Lightweight Markup Languages ============================ According to **Wikipedia**: > A [lightweight markup lan...